ViewGene
Locus Name:
GeneID:
Location:

GeneID:6669
TrivialName: PA14_58030
AnnotatorUID: danlee
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_58030
PAO1 Ortholog Locus:PA4470
Sequence Length:1377
Protein Length:458
Start: 5163507
Stop: 5162131
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07858.1|AE004860_14 (AE004860) fumarate hydratase [Pseudomonas aeruginosa PAO1]
Identities = 373/373 (100%), Positives = 373/373 (100%)
Sequence:
ATGACTGACACCCGCATCGAACGCGACAGCATGGGCGAACTGGCGGTCCCGGCGACCGCCCTCTATGGCGCC
CAGACCCAGCGCGCGGTGAACAACTTCCCGGTCAGCGGCCAGCGCATGCCCCAGGCCTTCGTCCGCGCCCTG
CTGCTGGCCAAGGCCGCGGCAGCGCGGGCGAACGTCTCCCTGCAGCAACTGGATGCACCGATGGGCGAGGCG
ATCGCCGAGACCTGCCTGCAGTTGCTGCAGGAGGACTTCATGCAGCATTTCCCGGTGGATGTGTTCCAGACC
GGCTCCGGCACCAGTTCCAACATGAACGCCAACGAAGTGGTGGCGACCCTGGCCAGTCGCCGCCTGGGCGGC
AAGGTCAATCCGAACGACCATGTGAACTGCGGGCAGAGCAGCAACGACATCATCCCCTCGACCATCCACATC
AGTGCCGCCCTCGAGATCAGCGAACGCCTGCTGCCGGCGCTGCGCCACCTGGAGCAGACTATCCAGAGCAAG
GCCGGCGAAGTGCATGCCTATGTGAAGACCGGCCGCACCCACCTGATGGATGCGATGCCGGTACGCATGAGC
CAGGTGCTCGGTGGCTGGGCGCAGCAGGTGCGACAGGCTGGCGTGCACATCGAGAGCGTACTTCCTGCCTTG
CAGCAGTTGGCACAGGGCGGCACCGCGGTGGGCACCGGGATCAACGCCCATCCGCGGTTCGCCGAACGTTTC
AGCCAGGAGCTGAACGACCTGACCGGGTTGGCGTTCCGCCCCGGCGACGACTTCTTCGCCCTGATCGGTTCG
CAGGACACGGCGGTCGCTGCGTCCGGCCAGTTGAAGACCCTGGCCGTGACCCTGATGAAGCTGGCCAACGAC
CTGCGCTGGATGAACTCCGGGCCGCTTGCCGGGCTCGGCGAGATCGAGCTGGAAGCGCTGCAACCAGGCTCC
TCGATCATGCCCGGCAAGGTCAACCCGGTGATCCCGGAGGCCACCGCGATGGTCGCCGCCCAGGTGATCGGC
AATGACGCCGCCATTGCCGTCGCCGGCCAATCGGGCAACTTCGAACTGAACGTGATGCTGCCGCTGGTGGCG
GACAACCTGTTGCACAGCATCCAGTTGCTGGCCAACGTCAGCCGGCTGCTGGCGGACAAGGCCATCGCCAGC
TTCAAGGTCAACCAGGGCAAGCTCAGCGAGGCGTTGGCGCGCAACCCGATCCTGGTCACTGCGCTGAACCCG
ATCATCGGCTACCAGAAGGCTGCGGAAATCGCCAAGCAGGCCTATCGCGAGGGACGGCCGATCATCGATGTG
GCGCTGGAAAACACCGATCTGGACCGTGCGCGCCTGGAGGTGTTGCTGGATCCGGAAAAACTCACGGCTGGC
GGCCTCTGa
Translation:
MTDTRIERDSMGELAVPATALYGAQTQRAVNNFPVSGQRMPQAFVRALLLAKAAAARANVSLQQLDAPMGEA
IAETCLQLLQEDFMQHFPVDVFQTGSGTSSNMNANEVVATLASRRLGGKVNPNDHVNCGQSSNDIIPSTIHI
SAALEISERLLPALRHLEQTIQSKAGEVHAYVKTGRTHLMDAMPVRMSQVLGGWAQQVRQAGVHIESVLPAL
QQLAQGGTAVGTGINAHPRFAERFSQELNDLTGLAFRPGDDFFALIGSQDTAVAASGQLKTLAVTLMKLAND
LRWMNSGPLAGLGEIELEALQPGSSIMPGKVNPVIPEATAMVAAQVIGNDAAIAVAGQSGNFELNVMLPLVA
DNLLHSIQLLANVSRLLADKAIASFKVNQGKLSEALARNPILVTALNPIIGYQKAAEIAKQAYREGRPIIDV
ALENTDLDRARLEVLLDPEKLTAGGL*
AnnotationID:6670GeneID:6669
AnnotatorUID: danlee
Modification Date/Time: 2005-07-11 13:01:55
Gene Name:fumC1
Confidence Code:1
GeneProduct:fumarate hydratase
Cell Localization:(1) Cytoplasmic
Synonyms:PA4470
Cell Localization Confidence Code:2
MolecularFunction:
Functional Category:(12) Energy metabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0114,COG1027,KOG1317
Secondary Functional Category(ies):
EC Number:4.2.1.2
Status:ACTIVE
Pathway:






 
Homology:
Identities = 1366/1377 (99%) with PA4470 (fumC1),






 
Structural Features:
COG0114, FumC, Fumarase [Energy production and conversion]
CD-Length = 462 residues,  81.8% aligned
Score =  543 bits (1400), Expect = 3e-155
Identities = 206/378 (54%), Positives = 259/378 (68%), Gaps = 6/378 (1%)

COG1027, AspA, Aspartate ammonia-lyase 
[Amino acid transport and metabolism]
CD-Length = 471 residues,  79.4% aligned
Score =  367 bits (943), Expect = 3e-102
Identities = 160/375 (42%), Positives = 218/375 (58%), Gaps = 7/375 (1%)

KOG1317, Fumarase [Energy production and conversion]
CD-Length = 487 residues, only  76.4% aligned
Score =  362 bits (929), Expect = 1e-100
Identities = 178/372 (47%), Positives = 243/372 (65%), Gaps = 5/372 (1%)






   
Genomic Context:






   
Comment:
Gene prediction error missed 5' end of ORF.  Proteomic data confirmed that ORF is full-length.
blastn to PAO1 for the new nucleotide sequence is now 1366/1377 (99%) along length of whole ORF.
Corrected 7-11-04.


















    ReferenceID:13103




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:30432




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31509




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:6669_cdd.html


    		




 
URL:

















    ReferenceID:32858




  
Author/Investigator(s):
        Hassett DJ, Howell ML, Ochsner UA, Vasil ML, Johnson Z, Dean GE.





  
Title:
        An operon containing fumC and sodA encoding fumarase C and manganese superoxide dismutase is controlled by the ferric uptake regulator in Pseudomonas aeruginosa: fur mutants produce elevated alginate levels.




  
PubMed:
        9045799


MedLine:
        




    
Source:
J Bacteriol. 1997 Mar;179(5):1452-9.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9045799

















    ReferenceID:32859




  
Author/Investigator(s):
        Hassett DJ, Howell ML, Sokol PA, Vasil ML, Dean GE.





  
Title:
        Fumarase C activity is elevated in response to iron deprivation and in mucoid, alginate-producing Pseudomonas aeruginosa: cloning and characterization of fumC and purification of native fumC.




  
PubMed:
        9045798


MedLine:
        




    
Source:
J Bacteriol. 1997 Mar;179(5):1442-51.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9045798

















    ReferenceID:32860




  
Author/Investigator(s):
        Polack B, Dacheux D, Delic-Attree I, Toussaint B, Vignais PM.





  
Title:
        The Pseudomonas aeruginosa fumc and soda genes belong to an iron-responsive operon.




  
PubMed:
        8806672


MedLine:
        




    
Source:
Biochem Biophys Res Commun. 1996 Sep 13;226(2):555-60.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8806672

















    ReferenceID:32861




  
Author/Investigator(s):
        Ochsner UA, Vasil ML.





  
Title:
        Gene repression by the ferric uptake regulator in Pseudomonas aeruginosa: cycle selection of iron-regulated genes.




  
PubMed:
        8633080


MedLine:
        




    
Source:
Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):4409-14.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8633080









           
Homologs By Global Alignment 

           

       



     
Gene ID:6669
           
Identity:

                               
                                   0%
                               
                                   10%
                               
                                   20%
                               
                                   30%
                               
                                   40%
                               
                                   50%
                               
                                   60%
                               
                                   70%
                               
                                   80%
                               
                                   90%
                               
                                   100%
                               
                             

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
8021
                           PA4470_tr
                           translation of PA4470
                           458
                           81.44
                           81.44
                           85
                           1861.0
     

     
     
201191
                           gb|AAG07858.1|AE004860_14
                           (AE004860) fumarate hydratase [Pseudomonas aeruginosa PAO1]
                           458
                           81.44
                           81.44
                           85
                           1861.0
     

     
     
201192
                           gb|AAB02830.1|
                           (U59458) fumarase C [Pseudomonas aeruginosa]
                           458
                           81.44
                           81.44
                           85
                           1861.0
     

     
     
201193
                           gb|AAB17389.1|
                           (U72494) fumarase [Pseudomonas aeruginosa]
                           466
                           78.96
                           78.96
                           94
                           1823.0
     

     
     
201196
                           gb|AAN66569.1|AE016285_7
                           (AE016777) fumarate hydratase, class II [Pseudomonas putida KT2440]
                           459
                           65.14
                           71.89
                           86
                           1507.0
     

     






      

          
GC ORFID: 49671How Found: Glimmer

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: Glimmer Score: 

          
Start: 4426931Stop: 4425810

          
Length: 1122


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGaTruncated Stop: 

          
Homolog: t_PA4470 translation of PA4470Homolog Bit Score 721.0

          
Other Homologs:  t_PA4470 translation of PA4470 (BLASTP 721), t_PA0854 translation of PA0854 (BLASTP 323), psyr_15may02_Scaffold8_revised_gene7700 related to: gi|15596051|ref|NP_249545.1| (NC_002516) fumarate hydratase [Pseudomonas aeruginosa] pir||H83538 fumarate hydratase PA0854 [imported] - Pseudomonas aeruginosa (strain PAO1) gb|AAG04243.1|AE004520_6 (AE004520) fumarate hydratase [Pseudomonas aerug-TRUNCATED- (BLASTP 318), t_PA5429 translation of PA5429 (BLASTP 256), psyr_15may02_Scaffold2_revised_gene2909 related to: gi|114273|sp|P07346|ASPA_PSEFL ASPARTATE AMMONIA-LYASE (ASPARTASE) pir||UFPSDF aspartate ammonia-lyase (EC 4.3.1.1) - Pseudomonas fluorescens emb|CAA28037.1| (X04441) aspartase (aa 1-478) [Pseudomonas fluorescens] dbj|BAA00062.1| (D00100) aspartase [Pseudo-TRUNCATED- (BLASTP 256)

          
GC ORF Sequence

           
ATGCAGCATTTCCCGGTGGATGTGTTCCAGACCGGCTCCGGCACCAGTTCCAACATGAACGCCAACGAAGTG 
GTGGCGACCCTGGCCAGTCGCCGCCTGGGCGGCAAGGTCAATCCGAACGACCATGTGAACTGCGGGCAGAGC 
AGCAACGACATCATCCCCTCGACCATCCACATCAGTGCCGCCCTCGAGATCAGCGAACGCCTGCTGCCGGCG 
CTGCGCCACCTGGAGCAGACTATCCAGAGCAAGGCCGGCGAAGTGCATGCCTATGTGAAGACCGGCCGCACC 
CACCTGATGGATGCGATGCCGGTACGCATGAGCCAGGTGCTCGGTGGCTGGGCGCAGCAGGTGCGACAGGCT 
GGCGTGCACATCGAGAGCGTACTTCCTGCCTTGCAGCAGTTGGCACAGGGCGGCACCGCGGTGGGCACCGGG 
ATCAACGCCCATCCGCGGTTCGCCGAACGTTTCAGCCAGGAGCTGAACGACCTGACCGGGTTGGCGTTCCGC 
CCCGGCGACGACTTCTTCGCCCTGATCGGTTCGCAGGACACGGCGGTCGCTGCGTCCGGCCAGTTGAAGACC 
CTGGCCGTGACCCTGATGAAGCTGGCCAACGACCTGCGCTGGATGAACTCCGGGCCGCTTGCCGGGCTCGGC 
GAGATCGAGCTGGAAGCGCTGCAACCAGGCTCCTCGATCATGCCCGGCAAGGTCAACCCGGTGATCCCGGAG 
GCCACCGCGATGGTCGCCGCCCAGGTGATCGGCAATGACGCCGCCATTGCCGTCGCCGGCCAATCGGGCAAC 
TTCGAACTGAACGTGATGCTGCCGCTGGTGGCGGACAACCTGTTGCACAGCATCCAGTTGCTGGCCAACGTC 
AGCCGGCTGCTGGCGGACAAGGCCATCGCCAGCTTCAAGGTCAACCAGGGCAAGCTCAGCGAGGCGTTGGCG 
CGCAACCCGATCCTGGTCACTGCGCTGAACCCGATCATCGGCTACCAGAAGGCTGCGGAAATCGCCAAGCAG 
GCCTATCGCGAGGGACGGCCGATCATCGATGTGGCGCTGGAAAACACCGATCTGGACCGTGCGCGCCTGGAG 
GTGTTGCTGGATCCGGAAAAACTCACGGCTGGCGGCCTCTGa